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AirwaySegmenter.cxx
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/*=============================================================================
// --- Airway Segmenter ---+
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
// Authors: Marc Niethammer, Yi Hong, Johan Andruejol
=============================================================================*/
// STL includes
#include <cmath>
#include <iostream>
#include <limits>
#include <map>
#include <string>
#include <time.h>
#include <vector>
//ITK includes
#include <itkAbsoluteValueDifferenceImageFilter.h>
#include <itkAddImageFilter.h>
#include <itkBinaryThresholdImageFilter.h>
#include <itkCastImageFilter.h>
#include <itkConnectedComponentImageFilter.h>
#include <itkImageDuplicator.h>
#include <itkFastMarchingImageFilter.h>
#include <itkImage.h>
#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkImageRegionConstIterator.h>
#include <itkImageSliceConstIteratorWithIndex.h>
#include <itkImageSliceIteratorWithIndex.h>
#include <itkIdentityTransform.h>
#include <itkLabelGeometryImageFilter.h>
#include <itkMaskImageFilter.h>
#include <itkMatrix.h>
#include <itkMultiplyImageFilter.h>
#include <itkOtsuThresholdImageFilter.h>
#include <itkRelabelComponentImageFilter.h>
#include <itkResampleImageFilter.h>
#include <itkSmartPointer.h>
#include <itkSpatialOrientationAdapter.h>
#include <itkSubtractImageFilter.h>
//Local includes
#include "AirwaySegmenterCLP.h"
#include "AirwaySegmenterConfig.h"
#include "itkAirwaySurfaceWriter.h"
#include "itkMaskedOtsuThresholdImageFilter.h"
namespace
{
int outputAllSettings(int argc, char* argv[])
{
PARSE_ARGS;
std::cout << "Parameter settings:" << std::endl;
std::cout << "-----------------------------------------" << std::endl;
std::cout << "input image = " << inputImage << std::endl;
std::cout << "output image = " << outputImage << std::endl;
std::cout << "output geometry = " << outputGeometry << std::endl;
std::cout << std::endl;
std::cout << "dMaxAirwayRadius = " << dMaxAirwayRadius << std::endl;
std::cout << "dErodeDistance = " << dErodeDistance << std::endl;
std::cout << "iMaximumNumberOfCVIterations = " << iMaximumNumberOfCVIterations << std::endl;
std::cout << "dCVLambda = " << dCVLambda << std::endl;
std::cout << "iComponent = " << iComponent << std::endl;
std::cout << "lowerSeed = " << lowerSeed[0]
<< ", " << lowerSeed[1]
<< ", " << lowerSeed[2]
<< std::endl;
std::cout << "lowerSeedRadius = " << lowerSeedRadius << std::endl;
std::cout << "upperSeed = " << upperSeed[0]
<< ", " << upperSeed[1]
<< ", " << upperSeed[2]
<< std::endl;
std::cout << "upperSeedRadius = " << upperSeedRadius << std::endl;
for (int i = 0; i < maxillarySinusesSeeds.size(); ++i)
{
std::cout << "maxillarySinusesSeeds = " << maxillarySinusesSeeds[i][0]
<< ", " << maxillarySinusesSeeds[i][1]
<< ", " << maxillarySinusesSeeds[i][2]
<< std::endl;
}
std::cout << "maxillarySinusesSeedsRadius = " << maxillarySinusesSeedsRadius << std::endl;
std::cout << "erosionPercentage = " << erosionPercentage << std::endl;
std::cout << "bRemoveMaxillarySinuses = " << bRemoveMaxillarySinuses << std::endl;
std::cout << "bNoWarning = " << bNoWarning <<std::endl;
std::cout << "bDebug = " << bDebug << std::endl;
std::cout << "sDebugFolder = " << sDebugFolder << std::endl;
std::cout << "bRAIImage = " << bRAIImage << std::endl;
std::cout << "sRAIImagePath = " << sRAIImagePath << std::endl;
std::cout << "-----------------------------------------" << std::endl;
std::cout << std::endl << std::endl << std::endl;
return 0;
}
//This Fast marching is factorised for preventing the memory to
//be overwhelmed by unused nodes. Now that
//This function is for internal use, it assumes all
// its parameters are given correctly
template<class T> itk::Image<float, 3>::Pointer
FastMarchIt(typename itk::Image<T, 3>::Pointer image,
std::string type, double erodedDistance, double airwayRadius)
{
//Necessaries typedefs
typedef itk::Image<float, 3> FloatImageType;
typedef itk::Image<T, 3> LabelImageType;
typedef itk::FastMarchingImageFilter<FloatImageType, FloatImageType> FastMarchingFilterType;
typedef typename FastMarchingFilterType::NodeContainer NodeContainer;
typedef typename FastMarchingFilterType::NodeType NodeType;
typedef itk::ImageRegionConstIterator<LabelImageType> ConstIteratorType;
//Instantiations
typename FastMarchingFilterType::Pointer fastMarching =
FastMarchingFilterType::New();
typename NodeContainer::Pointer seeds = NodeContainer::New();
seeds->Initialize();
//Nodes are created as stack variables and
//initialized with a value and an itk::Index position. NodeType node;
NodeType node;
// seed value is 0 for all of them, because these are all starting nodes
node.SetValue( 0.0 );
// loop through the output image
// and set all voxels to 0 seed voxels
ConstIteratorType it( image, image->GetLargestPossibleRegion() );
unsigned int uiNumberOfSeeds = 0;
for ( it.GoToBegin(); !it.IsAtEnd(); ++it )
{
if (type.compare("Out") == 0) //Dilatation
{
if ( it.Get() > 0 )
{
node.SetIndex( it.GetIndex() );
seeds->InsertElement( uiNumberOfSeeds++, node );
}
}
else if (type.compare("In") == 0)//Erosion
{
if ( it.Get() == 0 )
{
node.SetIndex( it.GetIndex() );
seeds->InsertElement( uiNumberOfSeeds++, node );
}
}
}
//The set of seed nodes is now passed to the
// FastMarchingImageFilter with the method SetTrialPoints().
fastMarching->SetTrialPoints( seeds );
// The FastMarchingImageFilter requires the user to specify
//the size of the image to be produced as output.
//This is done using the SetOutputSize().
fastMarching->SetInput( NULL );
fastMarching->SetSpeedConstant( 1.0 ); // to solve a simple Eikonal equation
fastMarching->SetOutputSize( image->GetBufferedRegion().GetSize() );
fastMarching->SetOutputRegion( image->GetBufferedRegion() );
fastMarching->SetOutputSpacing( image->GetSpacing() );
fastMarching->SetOutputOrigin( image->GetOrigin() );
fastMarching->SetStoppingValue( airwayRadius + erodedDistance + 1 );
try
{
fastMarching->Update();
}
catch(itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
return fastMarching->GetOutput();
}
//Look for the labels in the sphercal region within radius of
//the ball center and return the most represented label
template<class T> int
LabelIt(typename itk::Image<T, 3>::Pointer image,
std::vector<float> ballCenter, double radius, bool printLabels)
{
typedef itk::Image<T, 3> TImage;
typedef typename itk::Image<T, 3>::SizeType TSize;
typedef typename itk::Image<T, 3>::SpacingType TSpacing;
typedef typename itk::Image<T, 3>::PointType TOrigin;
typedef typename itk::Image<T, 3>::IndexType TIndex;
TOrigin imageOrigin = image->GetOrigin();
TSpacing imageSpacing = image->GetSpacing();
TSize imageSize = image->GetBufferedRegion().GetSize();
// Convert to LPS system
float x, y, z;
x = -ballCenter[0];
y = -ballCenter[1];
z = ballCenter[2];
//Get the bounding box around the piryna aperture
int region[6];
region[0] = int( floor( ( x - radius - imageOrigin[0] ) / imageSpacing[0] ) );
region[1] = int( floor( ( y - radius - imageOrigin[1] ) / imageSpacing[1] ) );
region[2] = int( floor( ( z - radius - imageOrigin[2] ) / imageSpacing[2] ) );
region[3] = int( ceil( ( x + radius - imageOrigin[0] ) / imageSpacing[0] ) );
region[4] = int( ceil( ( y + radius - imageOrigin[1] ) / imageSpacing[1] ) );
region[5] = int( ceil( ( z + radius - imageOrigin[2] ) / imageSpacing[2] ) );
region[0] = region[0] > 0 ? region[0] : 0;
region[1] = region[1] > 0 ? region[1] : 0;
region[2] = region[2] > 0 ? region[2] : 0;
region[3] = region[3] < (imageSize[0]-1) ? region[3] : (imageSize[0]-1);
region[4] = region[4] < (imageSize[1]-1) ? region[4] : (imageSize[1]-1);
region[5] = region[5] < (imageSize[2]-1) ? region[5] : (imageSize[2]-1);
if (printLabels)
{
std::cout << "Region: " << region[0] << ", "
<< region[1] << ", " << region[2] << ", "
<< region[3] << ", " << region[4] << ", "
<< region[5] << std::endl;
}
std::map<int, int> labels;
for( int iI=region[0]; iI<=region[3]; iI++ )
{
for( int iJ=region[1]; iJ<=region[4]; iJ++ )
{
for( int iK=region[2]; iK<=region[5]; iK++ )
{
//Get real space position
double iX = iI * imageSpacing[0] + imageOrigin[0] - x;
double iY = iJ * imageSpacing[1] + imageOrigin[1] - y;
double iZ = iK * imageSpacing[2] + imageOrigin[2] - z;
//If within the nose ball region
if( iX * iX + iY * iY + iZ * iZ <= radius * radius )
{
TIndex pixelIndex;
pixelIndex[0] = iI;
pixelIndex[1] = iJ;
pixelIndex[2] = iK;
int label = image->GetPixel( pixelIndex );
if( label != 0 )//ignore label 0, it's always the background
{
labels[label] += 1;
}
}
}
}
}
int finalLabel = 0;
int labelCount = 0;
for(std::map<int, int>::const_iterator it = labels.begin();
it != labels.end(); ++it)
{
if (printLabels)
{
std::cout<<"Labels "<<it->first<<" : "<<it->second<<std::endl;
}
if (it->second > labelCount)
{
labelCount = it->second;
finalLabel = it->first;
}
}
return finalLabel;
}
template<class T> int DoIt(int argc, char* argv[], T)
{
//--
//-- Typedefs
//--
typedef float TFloatType;
typedef T TPixelType;
typedef T TLabelPixelType;
const unsigned char DIMENSION = 3;
typedef itk::Image<TPixelType, DIMENSION> InputImageType;
typedef itk::Image<TPixelType, DIMENSION> OutputImageType;
typedef itk::Image<TLabelPixelType, DIMENSION> LabelImageType;
typedef itk::Image<TFloatType, DIMENSION> FloatImageType;
typedef itk::Image<unsigned char, DIMENSION> UCharImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typedef itk::ImageFileReader<LabelImageType> ReaderLabelType;
typedef itk::ImageFileWriter<OutputImageType> WriterType;
typedef itk::ImageFileWriter<LabelImageType> WriterLabelType;
typedef typename LabelImageType::SizeType TSize;
typedef typename LabelImageType::SpacingType TSpacing;
typedef typename LabelImageType::PointType TOrigin;
typedef typename LabelImageType::IndexType TIndex;
//--
//-- Parsing the input
//--
// parse the input arguments
PARSE_ARGS;
// output the arguments
if (bDebug)
{
outputAllSettings( argc, argv );
}
//Outputing debug result to current folder if not precised otherwise
if(bDebug &&
(sDebugFolder.compare("None") == 0 || sDebugFolder.compare("") == 0))
{
sDebugFolder = ".";
}
// read the input image
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( inputImage );
try
{
reader->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
//--
//-- Automatic Resampling to RAI
//--
typename InputImageType::Pointer originalImage = reader->GetOutput();
typename InputImageType::DirectionType originalImageDirection = originalImage->GetDirection();
itk::SpatialOrientationAdapter adapter;
typename InputImageType::DirectionType RAIDirection =
adapter.ToDirectionCosines(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);
bool shouldConvert = false;
for (int i = 0; i < 3; ++i)
{
for (int j = 0; j < 3; ++j)
{
if (abs(originalImageDirection[i][j] - RAIDirection[i][j]) > 1e-6)
{
shouldConvert = true;
break;
}
}
}
typedef itk::ResampleImageFilter<InputImageType, InputImageType> ResampleImageFilterType;
typename ResampleImageFilterType::Pointer resampleFilter = ResampleImageFilterType::New();
if (shouldConvert)
{
typedef itk::IdentityTransform<double, DIMENSION> IdentityTransformType;
resampleFilter->SetTransform(IdentityTransformType::New());
resampleFilter->SetInput(originalImage);
resampleFilter->SetSize(originalImage->GetLargestPossibleRegion().GetSize());
resampleFilter->SetOutputOrigin(originalImage->GetOrigin());
resampleFilter->SetOutputSpacing(originalImage->GetSpacing());
resampleFilter->Update();
originalImage = resampleFilter->GetOutput();
}
//Write RAI Image if asked to
if (bRAIImage)
{
typename WriterType::Pointer writer = WriterType::New();
writer->SetInput( originalImage);
writer->SetFileName( sRAIImagePath.c_str() );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
}
//--
//-- Otsu thresholding first
//--
typedef itk::OtsuThresholdImageFilter<InputImageType, LabelImageType > OtsuThresholdFilterType;
typename OtsuThresholdFilterType::Pointer otsuThresholdFilter =
OtsuThresholdFilterType::New();
otsuThresholdFilter->SetInsideValue( 0 );
otsuThresholdFilter->SetOutsideValue( 1 );
otsuThresholdFilter->SetInput( originalImage );
otsuThresholdFilter->Update();
if (bDebug)
{
typename WriterLabelType::Pointer writer = WriterLabelType::New();
writer->SetInput( otsuThresholdFilter->GetOutput() );
std::string filename = sDebugFolder;
filename += "/otsu.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl; std::cerr << excep << std::endl;
}
}
//--
//-- Dilatation
//--
typedef itk::BinaryThresholdImageFilter<FloatImageType, LabelImageType > ThresholdingFilterType;
typename ThresholdingFilterType::Pointer thresholdDilation = ThresholdingFilterType::New();
thresholdDilation->SetLowerThreshold( 0.0 );
thresholdDilation->SetUpperThreshold( dMaxAirwayRadius );
thresholdDilation->SetOutsideValue( 0 );
thresholdDilation->SetInsideValue( 1 );
//Custom Fast marching
typedef itk::FastMarchingImageFilter<FloatImageType, FloatImageType> FastMarchingFilterType;
typedef typename FastMarchingFilterType::NodeContainer NodeContainer;
typedef typename FastMarchingFilterType::NodeType NodeType;
typedef itk::ImageRegionConstIterator<LabelImageType> ConstIteratorType;
//Instantiations
typename FastMarchingFilterType::Pointer fastMarchingDilate = FastMarchingFilterType::New();
typename NodeContainer::Pointer trialSeeds = NodeContainer::New();
typename NodeContainer::Pointer aliveSeeds = NodeContainer::New();
trialSeeds->Initialize();
aliveSeeds->Initialize();
//Nodes are created as stack variables and
//initialized with a value and an itk::Index position. NodeType node;
NodeType node;
node.SetValue( 0.0 );
// loop through the output image
// and set all voxels to 0 seed voxels
ConstIteratorType binaryImageIterator( otsuThresholdFilter->GetOutput(),
otsuThresholdFilter->GetOutput()->GetLargestPossibleRegion() );
ConstIteratorType imageIterator( originalImage,
originalImage->GetLargestPossibleRegion() );
unsigned int uiNumberOfTrialSeeds = 0;
unsigned int uiNumberOfAliveSeeds = 0;
imageIterator.GoToBegin();
for ( binaryImageIterator.GoToBegin(); !binaryImageIterator.IsAtEnd(); ++binaryImageIterator )
{
if ( binaryImageIterator.Get() > 0 )
{
node.SetIndex( binaryImageIterator.GetIndex() );
if (imageIterator.Get() > 60) //alive seed
{
aliveSeeds->InsertElement( uiNumberOfAliveSeeds++, node );
}
else //trial seed
{
trialSeeds->InsertElement( uiNumberOfTrialSeeds++, node );
}
}
++imageIterator;
}
if (bDebug)
{
std::cout<<std::endl<<std::endl
<<"FastMarching Dilatation: Number of Alive Seeds: "<<aliveSeeds->Size()
<<std::endl
<<" Number of Trial Seeds: "<<trialSeeds->Size()
<<std::endl;
}
//The set of seed nodes is now passed to the
// FastMarchingImageFilter with the method SetTrialPoints().
fastMarchingDilate->SetTrialPoints( trialSeeds );
fastMarchingDilate->SetAlivePoints( aliveSeeds );
// The FastMarchingImageFilter requires the user to specify
//the size of the image to be produced as output.
//This is done using the SetOutputSize()
fastMarchingDilate->SetInput( NULL );
fastMarchingDilate->SetSpeedConstant( 1.0 ); // to solve a simple Eikonal equation
fastMarchingDilate->SetOutputSize( otsuThresholdFilter->GetOutput()->GetBufferedRegion().GetSize() );
fastMarchingDilate->SetOutputRegion( otsuThresholdFilter->GetOutput()->GetBufferedRegion() );
fastMarchingDilate->SetOutputSpacing( otsuThresholdFilter->GetOutput()->GetSpacing() );
fastMarchingDilate->SetOutputOrigin( otsuThresholdFilter->GetOutput()->GetOrigin() );
fastMarchingDilate->SetStoppingValue( dErodeDistance + dMaxAirwayRadius+ 1 );
try
{
fastMarchingDilate->Update();
}
catch(itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
if (bDebug)
{
typedef itk::ImageFileWriter<FloatImageType> WriterFloatType;
typename WriterFloatType::Pointer writer = WriterFloatType::New();
writer->SetInput( fastMarchingDilate->GetOutput() );
std::string filename = sDebugFolder;
filename += "/fmt-out.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
}
thresholdDilation->SetInput( fastMarchingDilate->GetOutput() );
thresholdDilation->Update();
// Now write this for test purposes
if (bDebug)
{
typename WriterLabelType::Pointer writer = WriterLabelType::New();
writer->SetInput( thresholdDilation->GetOutput() );
std::string filename = sDebugFolder;
filename += "/fmt-out.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl; std::cerr << excep << std::endl;
}
}
//--
//-- Erosion (Thus creating a closing)
//--
typename ThresholdingFilterType::Pointer thresholdClosing = ThresholdingFilterType::New();
thresholdClosing->SetLowerThreshold( 0.0 );
thresholdClosing->SetUpperThreshold( dMaxAirwayRadius );
thresholdClosing->SetOutsideValue( 1 );
thresholdClosing->SetInsideValue( 0 );
//Instantiations
typename FastMarchingFilterType::Pointer fastMarchingClose = FastMarchingFilterType::New();
trialSeeds->Initialize();
aliveSeeds->Initialize();
// loop through the output image
// and set all voxels to 0 seed voxels
typedef itk::ImageRegionConstIterator<FloatImageType> ConstFloatIteratorType;
ConstFloatIteratorType floatDilatedImageIterator( fastMarchingDilate->GetOutput(),
fastMarchingDilate->GetOutput()->GetLargestPossibleRegion() );
ConstIteratorType binaryDilatedImageIterator( thresholdDilation->GetOutput(),
thresholdDilation->GetOutput()->GetLargestPossibleRegion() );
uiNumberOfTrialSeeds = 0;
uiNumberOfAliveSeeds = 0;
floatDilatedImageIterator.GoToBegin();
for ( binaryDilatedImageIterator.GoToBegin(); !binaryDilatedImageIterator.IsAtEnd(); ++binaryDilatedImageIterator )
{
if ( binaryDilatedImageIterator.Get() == 0 )
{
node.SetIndex( binaryDilatedImageIterator.GetIndex() );
if (floatDilatedImageIterator.Get() > dMaxAirwayRadius + dErodeDistance) //alive seed
{
aliveSeeds->InsertElement( uiNumberOfAliveSeeds++, node );
}
else //trial seed
{
trialSeeds->InsertElement( uiNumberOfTrialSeeds++, node );
}
}
++floatDilatedImageIterator;
}
if (bDebug)
{
std::cout<<std::endl<<std::endl
<<"FastMarching Close: Number of Alive Seeds: "<<aliveSeeds->Size()<<" "<<uiNumberOfAliveSeeds
<<std::endl
<<" Number of Trial Seeds: "<<trialSeeds->Size()<<" "<<uiNumberOfTrialSeeds
<<std::endl;
}
//The set of seed nodes is now passed to the
// FastMarchingImageFilter with the method SetTrialPoints().
fastMarchingClose->SetTrialPoints( trialSeeds );
fastMarchingClose->SetAlivePoints( aliveSeeds );
// The FastMarchingImageFilter requires the user to specify
//the size of the image to be produced as output.
//This is done using the SetOutputSize().
fastMarchingClose->SetInput( NULL );
fastMarchingClose->SetSpeedConstant( 1.0 ); // to solve a simple Eikonal equation
fastMarchingClose->SetOutputSize( thresholdDilation->GetOutput()->GetBufferedRegion().GetSize() );
fastMarchingClose->SetOutputRegion( thresholdDilation->GetOutput()->GetBufferedRegion() );
fastMarchingClose->SetOutputSpacing( thresholdDilation->GetOutput()->GetSpacing() );
fastMarchingClose->SetOutputOrigin( thresholdDilation->GetOutput()->GetOrigin() );
fastMarchingClose->SetStoppingValue( dErodeDistance + dMaxAirwayRadius+ 1 );
try
{
fastMarchingClose->Update();
}
catch(itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
if (bDebug)
{
typedef itk::ImageFileWriter<FloatImageType> WriterFloatType;
typename WriterFloatType::Pointer writer = WriterFloatType::New();
writer->SetInput( fastMarchingClose->GetOutput() );
std::string filename = sDebugFolder;
filename += "/fmt-out.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
}
thresholdClosing->SetInput( fastMarchingClose->GetOutput() );
thresholdClosing->Update();
// Now write this for test purposes
if (bDebug)
{
typename WriterLabelType::Pointer writer = WriterLabelType::New();
writer->SetInput( thresholdClosing->GetOutput() );
std::string filename = sDebugFolder;
filename += "/fmtIn-out.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl; std::cerr << excep << std::endl;
}
}
//--
//-- Difference between closed image and ostu-threshold of the original one
//--
typedef itk::AbsoluteValueDifferenceImageFilter<LabelImageType,
LabelImageType,
LabelImageType >
TAbsoluteValueDifferenceFilter;
typename TAbsoluteValueDifferenceFilter::Pointer absoluteValueDifferenceFilter
= TAbsoluteValueDifferenceFilter::New();
absoluteValueDifferenceFilter->SetInput1( otsuThresholdFilter->GetOutput() );
absoluteValueDifferenceFilter->SetInput2( thresholdClosing->GetOutput() );
absoluteValueDifferenceFilter->Update();
if (bDebug)
{
typename WriterLabelType::Pointer writer = WriterLabelType::New();
writer->SetInput( absoluteValueDifferenceFilter->GetOutput() );
std::string filename = sDebugFolder;
filename += "/avd.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
}
//--
//-- Create a sligthly eroded version of the closed image
//-- This is to prevent any weird effects at the outside of the face
//--
// We can get this simply by taking a
// slightly different threshold for the marching in case
typename ThresholdingFilterType::Pointer thresholdDifference =
ThresholdingFilterType::New();
thresholdDifference->SetLowerThreshold( 0.0 );
thresholdDifference->SetUpperThreshold( dMaxAirwayRadius+dErodeDistance );
thresholdDifference->SetOutsideValue( 1 );
thresholdDifference->SetInsideValue( 0 );
//The closed image was the input of the closing threshold
// (we don't want to re-run a fast marching)
thresholdDifference->SetInput( thresholdClosing->GetInput() );
// now do the masking
typedef itk::MaskImageFilter<LabelImageType,
LabelImageType,
LabelImageType > TMaskImageFilter;
typename TMaskImageFilter::Pointer absoluteValueDifferenceFilterMasked =
TMaskImageFilter::New();
absoluteValueDifferenceFilterMasked->SetInput1(
absoluteValueDifferenceFilter->GetOutput() );
absoluteValueDifferenceFilterMasked->SetInput2(
thresholdDifference->GetOutput() ); // second input is the mask
//--
//-- Extract largest component of the difference
//--
//(which should be -- hopefully -- the airway,
// since it was adapted to the expected size)
if (bDebug)
{
std::cout << "Extracting largest connected component ... ";
}
typedef itk::ConnectedComponentImageFilter<LabelImageType, LabelImageType > ConnectedComponentType;
typedef itk::RelabelComponentImageFilter<LabelImageType, LabelImageType > RelabelComponentType;
typedef itk::BinaryThresholdImageFilter<LabelImageType, LabelImageType > FinalThresholdingFilterType;
typename ConnectedComponentType::Pointer connected = ConnectedComponentType::New();
typename RelabelComponentType::Pointer relabel = RelabelComponentType::New();
typename FinalThresholdingFilterType::Pointer largestComponentThreshold =
FinalThresholdingFilterType::New();
// Label the components in the image and relabel them so that object
// numbers increase as the size of the objects decrease.
connected->SetInput ( absoluteValueDifferenceFilterMasked->GetOutput());
relabel->SetInput( connected->GetOutput() );
relabel->SetNumberOfObjectsToPrint( 5 );
relabel->Update();
int componentNumber = 0;
if (iComponent <= 0)
{
componentNumber = LabelIt<T>(relabel->GetOutput(),
lowerSeed,
lowerSeedRadius,
bDebug);
//std::cout<<"Label found = "<<componentNumber<<std::endl;
}
else
{
componentNumber = iComponent;
}
// pull out the largest object
largestComponentThreshold->SetInput( relabel->GetOutput() );
largestComponentThreshold->SetLowerThreshold( componentNumber ); // object #1
largestComponentThreshold->SetUpperThreshold( componentNumber ); // object #1
largestComponentThreshold->SetInsideValue(1);
largestComponentThreshold->SetOutsideValue(0);
largestComponentThreshold->Update();
if (bDebug)
{
typename WriterLabelType::Pointer lccWriter = WriterLabelType::New();
lccWriter->SetInput( largestComponentThreshold->GetOutput() );
std::string filename = sDebugFolder;
filename += "/lcc.nhdr";
lccWriter->SetFileName( filename );
try
{
lccWriter->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
std::cout << "done." << std::endl;
}
//--
//-- Now do another Otsu thresholding but just around the current segmentation
//--
// For this, we need to make it first a little bit bigger
typename ThresholdingFilterType::Pointer thresholdExtendedSegmentation =
ThresholdingFilterType::New();
//There are enough few seeds that they can all be considered as part of the trial seeds
thresholdExtendedSegmentation->SetInput( FastMarchIt<T>(
largestComponentThreshold->GetOutput(),
"Out",
dErodeDistance,
dMaxAirwayRadius) );
thresholdExtendedSegmentation->SetLowerThreshold( 0.0 );
// to make sure we get roughly twice the volume if the object would have a circular
// cross section;
// TODO: maybe make this a command line argument?
thresholdExtendedSegmentation->SetUpperThreshold( (sqrt(2.0)-1)*dMaxAirwayRadius );
thresholdExtendedSegmentation->SetOutsideValue( 0 );
thresholdExtendedSegmentation->SetInsideValue( 1 );
// force it so we have the mask available
thresholdExtendedSegmentation->Update();
if (bDebug)
{
typename WriterLabelType::Pointer writer = WriterLabelType::New();
writer->SetInput( thresholdExtendedSegmentation->GetOutput() );
std::string filename = sDebugFolder;
filename += "/seg-extended.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
}
// now do another Otsu thresholding
// but restrict the statistics to the currently obtained area
//(custom ostu-threshold filter)
typedef itk::MaskedOtsuThresholdImageFilter<InputImageType,
LabelImageType,
LabelImageType >
MaskedOtsuThresholdFilterType;
typename MaskedOtsuThresholdFilterType::Pointer maskedOtsuThresholdFilter =
MaskedOtsuThresholdFilterType::New();
// TODO: not sure about these inside/outside settings, check!!
maskedOtsuThresholdFilter->SetInsideValue( 1 );
maskedOtsuThresholdFilter->SetOutsideValue( 0 );
maskedOtsuThresholdFilter->SetMaskImage(
thresholdExtendedSegmentation->GetOutput() );
maskedOtsuThresholdFilter->SetInput( originalImage );
maskedOtsuThresholdFilter->Update();
// write it out to see if it worked (if it did clean up the code)
// write it out
if (bDebug)
{
typename WriterLabelType::Pointer labelWriterMaskedOtsu =
WriterLabelType::New();
labelWriterMaskedOtsu->SetInput( maskedOtsuThresholdFilter->GetOutput() );
std::string filename = sDebugFolder;
filename += "/otst-out-masked.nhdr";
labelWriterMaskedOtsu->SetFileName( filename );
try
{
labelWriterMaskedOtsu->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
}
//--
//-- Now mask it again and extract the largest component
//--
if (bDebug)
{
std::cout << " mask it again and extract the largest component ... " << std::endl;
}
typename TMaskImageFilter::Pointer maskedOtsu = TMaskImageFilter::New();
maskedOtsu->SetInput1( maskedOtsuThresholdFilter->GetOutput() );
maskedOtsu->SetInput2( thresholdDifference->GetOutput() ); // second input is the mask
if (bDebug)
{
typename WriterLabelType::Pointer writer = WriterLabelType::New();
writer->SetInput( maskedOtsu->GetOutput() );
std::string filename = sDebugFolder;
filename += "/maskedOtsu-out_second.nhdr";
writer->SetFileName( filename );
try
{
writer->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl; std::cerr << excep << std::endl;
}
std::cout << " Update ... " << std::endl;
}
try
{
maskedOtsu->Update();
}
catch ( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
return EXIT_FAILURE;
}
//--
//-- extract largest the airway with the lungs
//--
if (bDebug)
{
std::cout << "Extracting final largest connected component ... ";
}
typename ConnectedComponentType::Pointer connectedFinal =
ConnectedComponentType::New();
typename RelabelComponentType::Pointer relabelFinal =
RelabelComponentType::New();
typename FinalThresholdingFilterType::Pointer finalThreshold =